<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="application/xhtml+xml; charset=UTF-8" />
<title>GenomeTools - manual page for GT-COMPREADS-REFCOMPRESS(1)</title>
<link rel="stylesheet" type="text/css" href="style.css">
<link rel="stylesheet" href="..//style.css" type="text/css" />
</head>
<body>
<div id="menu">
<ul>
<li><a href="../index.html">Overview</a></li>
<li><a href="https://github.com/genometools/genometools/releases">Releases</a></li>
<li><a href="pub/">Archive</a></li>
<li><a href="https://github.com/genometools/genometools">Browse source</a></li>
<li><a href="http://github.com/genometools/genometools/issues/">Issue tracker</a></li>
<li><a href="../documentation.html">Documentation</a></li>
  <ul class="submenu">
    <li><a id="current" href="../tools.html">Tools</a></li>
    <li><a href="../manuals.html">Manuals</a></li>
    <li><a href="../libgenometools.html">C API</a></li>
    <li><a href="../docs.html"><tt>gtscript</tt> docs</a></li>
    <li><a href="../contract.html">Development Contract</a></li>
    <li><a href="../contribute.html">Contribute</a></li>
  </ul>
<li><a href="../annotationsketch.html"><tt>AnnotationSketch</tt></a></li>
<li><a href="../cgi-bin/gff3validator.cgi">GFF3 validator</a></li>
<li><a href="../license.html">License</a></li>
</ul>
</div>
<div id="main">
<div class="sect1">
<h2 id="_name">NAME</h2>
<div class="sectionbody">
<div class="paragraph"><p>gt-compreads-refcompress - Generates compact encoding for fastq data using Reference Compressed Reads (RCR).</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_synopsis">SYNOPSIS</h2>
<div class="sectionbody">
<div class="paragraph"><p><strong>gt compreads refcompress</strong> [option &#8230;] (-bam file -ref file)</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_description">DESCRIPTION</h2>
<div class="sectionbody">
<div class="dlist"><dl>
<dt class="hdlist1">
<strong>-v</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
be verbose (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-mquals</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
store mapping quality for each read (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-quals</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
store all quality values for each read, this implies enabling of option "vquals" (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-vquals</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
store quality values of read positions having variations compared to reference (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-descs</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
store read name for each read (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-ureads</strong> [<em>yes|no</em>]
</dt>
<dd>
<p>
store unmapped reads in a separated fastq file (base name will be the value given in name and suffix will be " _unmapped.fastq" (default: no)
</p>
</dd>
<dt class="hdlist1">
<strong>-ref</strong> [<em>string</em>]
</dt>
<dd>
<p>
Index file (generated by the gt encseq tool) for reference genome. (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-bam</strong> [<em>string</em>]
</dt>
<dd>
<p>
File containing alignment of reads to genome (sorted ".bam" file). (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-name</strong> [<em>string</em>]
</dt>
<dd>
<p>
specify base name for RCR to be generated. If not set, base name will be set to base name of value given for option "bam" (default: undefined)
</p>
</dd>
<dt class="hdlist1">
<strong>-help</strong> 
</dt>
<dd>
<p>
display help and exit
</p>
</dd>
<dt class="hdlist1">
<strong>-version</strong> 
</dt>
<dd>
<p>
display version information and exit
</p>
</dd>
</dl></div>
</div>
</div>
<div class="sect1">
<h2 id="_reporting_bugs">REPORTING BUGS</h2>
<div class="sectionbody">
<div class="paragraph"><p>Report bugs to <a href="https://github.com/genometools/genometools/issues">https://github.com/genometools/genometools/issues</a>.</p></div>
</div>
</div>
<div id="footer">
Copyright &copy; 2007-2023 The <i>GenomeTools</i> authors.
</div>
</div>
</body>
</html>
